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Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
ZYX ENST00000322764 69.73 57.73 65.19 0.53 0.57 0.53 0.95 1.46 1.29
CXorf65 ENST00000374251 69.74 20.69 43.58 0.53 1.47 0.62 0.95 0.79 2.01
TMIGD1 ENST00000328886 69.74 76.71 76.31 0.53 0.40 0.35 0.95 0.83 0.61
PLEKHH3 ENST00000591022 69.75 40.17 54.51 0.53 0.61 0.57 0.95 1.73 1.75
UGT1A7 ENST00000373426 69.75 78.20 77.12 0.53 0.43 0.37 0.95 0.74 0.59
ECHDC3 ENST00000379215 69.76 88.52 82.56 0.53 0.23 0.32 0.95 0.36 0.43
NRBP2 ENST00000442628 69.76 24.92 46.06 0.52 1.32 0.68 0.95 1.07 1.97
LNP1 ENST00000383693 69.77 87.67 82.10 0.52 0.24 0.35 0.95 0.36 0.46
HEXB ENST00000261416 69.77 48.05 59.08 0.52 0.63 0.49 0.95 2.00 1.68
ANKLE2 ENST00000357997 69.78 44.56 57.05 0.52 0.65 0.51 0.95 1.97 1.71
OR4B1 ENST00000309562 69.78 86.03 81.25 0.52 0.25 0.38 0.95 0.43 0.48
RGR ENST00000359452 69.79 85.38 80.92 0.52 0.25 0.39 0.95 0.45 0.51
SEPP1 ENST00000514985 69.79 61.00 67.16 0.52 0.54 0.52 0.95 1.41 1.17
NME8 ENST00000199447 69.80 72.98 74.26 0.52 0.51 0.39 0.95 1.03 0.69
C11orf1 ENST00000260276 69.81 90.64 83.60 0.52 0.25 0.33 0.95 0.36 0.40
UAP1L1 ENST00000409858 69.81 59.49 66.37 0.53 0.51 0.53 0.95 1.40 1.20
P2RX2 ENST00000343948 69.82 77.92 77.01 0.53 0.42 0.37 0.95 0.79 0.61
AFAP1 ENST00000420658 69.82 33.41 50.65 0.53 0.84 0.66 0.95 1.52 1.85
GPR111 ENST00000296862 69.83 90.52 83.53 0.53 0.25 0.33 0.95 0.37 0.40
RPGRIP1 ENST00000400017 69.83 43.48 56.47 0.53 0.61 0.52 0.95 1.96 1.70
UPP2 ENST00000605860 69.84 48.16 59.18 0.53 0.63 0.49 0.95 1.97 1.68
DALRD3 ENST00000341949 69.84 65.09 69.69 0.53 0.51 0.44 0.95 1.24 0.95
OR52I2 ENST00000312614 69.85 49.17 59.91 0.53 0.66 0.49 0.95 2.04 1.63
EIF3C ENST00000331666 69.85 91.13 83.85 0.54 0.24 0.34 0.95 0.35 0.42
ESPN ENST00000377828 69.86 48.77 59.62 0.54 0.63 0.49 0.95 2.01 1.68

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